Job ID = 2590462 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,702,669 reads read : 17,405,338 reads written : 8,702,669 reads 0-length : 8,702,669 spots read : 8,688,608 reads read : 17,377,216 reads written : 8,688,608 reads 0-length : 8,688,608 spots read : 8,726,350 reads read : 17,452,700 reads written : 8,726,350 reads 0-length : 8,726,350 spots read : 8,771,846 reads read : 17,543,692 reads written : 8,771,846 reads 0-length : 8,771,846 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:22 34889473 reads; of these: 34889473 (100.00%) were unpaired; of these: 1038366 (2.98%) aligned 0 times 26321744 (75.44%) aligned exactly 1 time 7529363 (21.58%) aligned >1 times 97.02% overall alignment rate Time searching: 00:11:22 Overall time: 00:11:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 4361685 / 33851107 = 0.1288 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 22:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 22:17:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:17:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:17:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 22:17:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:17:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:17:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 22:17:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:17:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:17:08: 1000000 INFO @ Mon, 12 Aug 2019 22:17:09: 1000000 INFO @ Mon, 12 Aug 2019 22:17:09: 1000000 INFO @ Mon, 12 Aug 2019 22:17:16: 2000000 INFO @ Mon, 12 Aug 2019 22:17:16: 2000000 INFO @ Mon, 12 Aug 2019 22:17:17: 2000000 INFO @ Mon, 12 Aug 2019 22:17:23: 3000000 INFO @ Mon, 12 Aug 2019 22:17:24: 3000000 INFO @ Mon, 12 Aug 2019 22:17:25: 3000000 INFO @ Mon, 12 Aug 2019 22:17:30: 4000000 INFO @ Mon, 12 Aug 2019 22:17:31: 4000000 INFO @ Mon, 12 Aug 2019 22:17:32: 4000000 INFO @ Mon, 12 Aug 2019 22:17:37: 5000000 INFO @ Mon, 12 Aug 2019 22:17:38: 5000000 INFO @ Mon, 12 Aug 2019 22:17:39: 5000000 INFO @ Mon, 12 Aug 2019 22:17:43: 6000000 INFO @ Mon, 12 Aug 2019 22:17:45: 6000000 INFO @ Mon, 12 Aug 2019 22:17:46: 6000000 INFO @ Mon, 12 Aug 2019 22:17:50: 7000000 INFO @ Mon, 12 Aug 2019 22:17:53: 7000000 INFO @ Mon, 12 Aug 2019 22:17:54: 7000000 INFO @ Mon, 12 Aug 2019 22:17:57: 8000000 INFO @ Mon, 12 Aug 2019 22:18:00: 8000000 INFO @ Mon, 12 Aug 2019 22:18:01: 8000000 INFO @ Mon, 12 Aug 2019 22:18:03: 9000000 INFO @ Mon, 12 Aug 2019 22:18:07: 9000000 INFO @ Mon, 12 Aug 2019 22:18:08: 9000000 INFO @ Mon, 12 Aug 2019 22:18:10: 10000000 INFO @ Mon, 12 Aug 2019 22:18:14: 10000000 INFO @ Mon, 12 Aug 2019 22:18:15: 10000000 INFO @ Mon, 12 Aug 2019 22:18:18: 11000000 INFO @ Mon, 12 Aug 2019 22:18:21: 11000000 INFO @ Mon, 12 Aug 2019 22:18:22: 11000000 INFO @ Mon, 12 Aug 2019 22:18:26: 12000000 INFO @ Mon, 12 Aug 2019 22:18:29: 12000000 INFO @ Mon, 12 Aug 2019 22:18:30: 12000000 INFO @ Mon, 12 Aug 2019 22:18:35: 13000000 INFO @ Mon, 12 Aug 2019 22:18:36: 13000000 INFO @ Mon, 12 Aug 2019 22:18:37: 13000000 INFO @ Mon, 12 Aug 2019 22:18:43: 14000000 INFO @ Mon, 12 Aug 2019 22:18:43: 14000000 INFO @ Mon, 12 Aug 2019 22:18:44: 14000000 INFO @ Mon, 12 Aug 2019 22:18:51: 15000000 INFO @ Mon, 12 Aug 2019 22:18:51: 15000000 INFO @ Mon, 12 Aug 2019 22:18:52: 15000000 INFO @ Mon, 12 Aug 2019 22:18:58: 16000000 INFO @ Mon, 12 Aug 2019 22:18:59: 16000000 INFO @ Mon, 12 Aug 2019 22:19:00: 16000000 INFO @ Mon, 12 Aug 2019 22:19:05: 17000000 INFO @ Mon, 12 Aug 2019 22:19:07: 17000000 INFO @ Mon, 12 Aug 2019 22:19:08: 17000000 INFO @ Mon, 12 Aug 2019 22:19:13: 18000000 INFO @ Mon, 12 Aug 2019 22:19:14: 18000000 INFO @ Mon, 12 Aug 2019 22:19:16: 18000000 INFO @ Mon, 12 Aug 2019 22:19:20: 19000000 INFO @ Mon, 12 Aug 2019 22:19:21: 19000000 INFO @ Mon, 12 Aug 2019 22:19:23: 19000000 INFO @ Mon, 12 Aug 2019 22:19:27: 20000000 INFO @ Mon, 12 Aug 2019 22:19:28: 20000000 INFO @ Mon, 12 Aug 2019 22:19:30: 20000000 INFO @ Mon, 12 Aug 2019 22:19:34: 21000000 INFO @ Mon, 12 Aug 2019 22:19:35: 21000000 INFO @ Mon, 12 Aug 2019 22:19:36: 21000000 INFO @ Mon, 12 Aug 2019 22:19:41: 22000000 INFO @ Mon, 12 Aug 2019 22:19:42: 22000000 INFO @ Mon, 12 Aug 2019 22:19:43: 22000000 INFO @ Mon, 12 Aug 2019 22:19:48: 23000000 INFO @ Mon, 12 Aug 2019 22:19:49: 23000000 INFO @ Mon, 12 Aug 2019 22:19:49: 23000000 INFO @ Mon, 12 Aug 2019 22:19:56: 24000000 INFO @ Mon, 12 Aug 2019 22:19:56: 24000000 INFO @ Mon, 12 Aug 2019 22:19:57: 24000000 INFO @ Mon, 12 Aug 2019 22:20:03: 25000000 INFO @ Mon, 12 Aug 2019 22:20:04: 25000000 INFO @ Mon, 12 Aug 2019 22:20:05: 25000000 INFO @ Mon, 12 Aug 2019 22:20:09: 26000000 INFO @ Mon, 12 Aug 2019 22:20:11: 26000000 INFO @ Mon, 12 Aug 2019 22:20:12: 26000000 INFO @ Mon, 12 Aug 2019 22:20:18: 27000000 INFO @ Mon, 12 Aug 2019 22:20:19: 27000000 INFO @ Mon, 12 Aug 2019 22:20:20: 27000000 INFO @ Mon, 12 Aug 2019 22:20:26: 28000000 INFO @ Mon, 12 Aug 2019 22:20:27: 28000000 INFO @ Mon, 12 Aug 2019 22:20:28: 28000000 INFO @ Mon, 12 Aug 2019 22:20:35: 29000000 INFO @ Mon, 12 Aug 2019 22:20:35: 29000000 INFO @ Mon, 12 Aug 2019 22:20:35: 29000000 INFO @ Mon, 12 Aug 2019 22:20:38: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:20:38: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:20:38: #1 total tags in treatment: 29489422 INFO @ Mon, 12 Aug 2019 22:20:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:20:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:20:39: #1 tags after filtering in treatment: 29489422 INFO @ Mon, 12 Aug 2019 22:20:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:20:39: #1 finished! INFO @ Mon, 12 Aug 2019 22:20:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:20:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:20:39: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:20:39: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:20:39: #1 total tags in treatment: 29489422 INFO @ Mon, 12 Aug 2019 22:20:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:20:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:20:40: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:20:40: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:20:40: #1 total tags in treatment: 29489422 INFO @ Mon, 12 Aug 2019 22:20:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:20:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:20:40: #1 tags after filtering in treatment: 29489422 INFO @ Mon, 12 Aug 2019 22:20:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:20:40: #1 finished! INFO @ Mon, 12 Aug 2019 22:20:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:20:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:20:40: #1 tags after filtering in treatment: 29489422 INFO @ Mon, 12 Aug 2019 22:20:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:20:40: #1 finished! INFO @ Mon, 12 Aug 2019 22:20:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:20:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:20:42: #2 number of paired peaks: 103 WARNING @ Mon, 12 Aug 2019 22:20:42: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Mon, 12 Aug 2019 22:20:42: start model_add_line... INFO @ Mon, 12 Aug 2019 22:20:42: start X-correlation... INFO @ Mon, 12 Aug 2019 22:20:42: end of X-cor INFO @ Mon, 12 Aug 2019 22:20:42: #2 finished! INFO @ Mon, 12 Aug 2019 22:20:42: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 22:20:42: #2 alternative fragment length(s) may be 2,42,553,581 bps INFO @ Mon, 12 Aug 2019 22:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.05_model.r WARNING @ Mon, 12 Aug 2019 22:20:42: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:20:42: #2 You may need to consider one of the other alternative d(s): 2,42,553,581 WARNING @ Mon, 12 Aug 2019 22:20:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:20:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:20:42: #2 number of paired peaks: 103 WARNING @ Mon, 12 Aug 2019 22:20:42: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Mon, 12 Aug 2019 22:20:42: start model_add_line... INFO @ Mon, 12 Aug 2019 22:20:42: start X-correlation... INFO @ Mon, 12 Aug 2019 22:20:42: end of X-cor INFO @ Mon, 12 Aug 2019 22:20:42: #2 finished! INFO @ Mon, 12 Aug 2019 22:20:42: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 22:20:42: #2 alternative fragment length(s) may be 2,42,553,581 bps INFO @ Mon, 12 Aug 2019 22:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.10_model.r WARNING @ Mon, 12 Aug 2019 22:20:42: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:20:42: #2 You may need to consider one of the other alternative d(s): 2,42,553,581 WARNING @ Mon, 12 Aug 2019 22:20:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:20:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:20:43: #2 number of paired peaks: 103 WARNING @ Mon, 12 Aug 2019 22:20:43: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Mon, 12 Aug 2019 22:20:43: start model_add_line... INFO @ Mon, 12 Aug 2019 22:20:43: start X-correlation... INFO @ Mon, 12 Aug 2019 22:20:43: end of X-cor INFO @ Mon, 12 Aug 2019 22:20:43: #2 finished! INFO @ Mon, 12 Aug 2019 22:20:43: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 22:20:43: #2 alternative fragment length(s) may be 2,42,553,581 bps INFO @ Mon, 12 Aug 2019 22:20:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.20_model.r WARNING @ Mon, 12 Aug 2019 22:20:43: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:20:43: #2 You may need to consider one of the other alternative d(s): 2,42,553,581 WARNING @ Mon, 12 Aug 2019 22:20:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:20:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:20:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:21:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:21:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:21:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:22:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:22:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:22:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.05_summits.bed INFO @ Mon, 12 Aug 2019 22:22:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2450 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:22:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:22:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:22:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.10_summits.bed INFO @ Mon, 12 Aug 2019 22:22:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1065 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981693/SRX3981693.20_summits.bed INFO @ Mon, 12 Aug 2019 22:22:23: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。